AIM: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS). METHODOLOGY: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified...

Two isolates representing a new species of Scheffersomyces were isolated from rotting wood samples collected in an Amazonian forest ecosystem in Brazil. Analysis of the sequences of the D1/D2 domains showed that this new species is phylogenetically related to Scheffersomyces NYMU 15730, a species without a formal description, and the two are in an early emerging position with respect to the xylose-fermenting subclade containing Scheffersomyces titanus and Scheffersomyces stipitis. Phylogenomic analyses using 474 orthologous genes placed the new species in an intermediary position between Scheffersomyces species and the larger genus Spathaspora and the Candida albicans/Lodderomyces clade...

Current HIV-1 epidemic in China is featured by diverse subtypes and continual emergence of new recombinant viruses. This study identified a novel unique recombinant form (URF) JL16013 among men who has sex with men (MSM) in Jilin, China. The JL16013 virus was different from all known subtypes and set up a distinct branch on the phylogenetic tree. This virus had a CRF01_AE backbone with two subtype B' fragments and one CRF65_cpx fragment inserted into gag, pol, env and nef regions, suggesting that this novel URF might originated from the CRF01_AE, subtype B' and CRF65_cpx viruses that were co-circulating in Jilin province...

A macluravirus, tentatively named alpinia oxyphylla mosaic virus (AloMV), was identified in Alpinia oxyphylla, and its complete genomic sequence determined. The positively single-stranded RNA genome is comprised of 8213 nucleotides excluding the poly (A) tail, and contains one large open reading frame encoding a polyprotein of 2,626 amino acids. Blastp search showed that the polyprotein of AloMV shared 48%~68% aa sequence identities with other reported macluraviruses. Phylogenetic analysis based on the nucleotide sequence of the polyprotein showed that AloMV, together with all other macluraviruses, clustered into the same group most closely related to cardamom mosaic virus, sharing 66...

The DECS (dsRNA isolation, exhaustive amplification, cloning and sequencing) analysis technique for viral diagnosis detected a tombusvirus in Japanese gentian not displaying severe symptoms. We tentatively named this virus "gentian virus A" (GeVA). GeVA systemically but inefficiently infected Japanese gentian without causing visible symptoms, while it led to severe symptoms in some other plants. The complete genome sequence of GeVA indicated a typical tombusvirus-like structure. Phylogenetic analysis of the deduced amino acid sequences of four tombusvirus-encoded proteins did not reveal other known tombusviruses that were closely-related to GeVA, suggesting that it is a novel tombusvirus...

The Triatominae subfamily is composed of 153 hematophagous species that are potential vectors of Trypanosoma cruzi , the etiological agent of Chagas disease. Karyotypic studies in triatomines were initiated in 1909. There are 92 karyotypes described, all grouped into the tribes Rhodniini and Triatomini. Recently, a phylogenetic study of the triatomines that combines molecular data with geological changes was performed. We now discuss how the karyotype evolved with the diversification of the triatomines.

The coexistence of phylogenetically related species is an attractive topic because of the potentially intense interspecific competition. The most often investigated mechanisms mediating coexistence of these species are environmental filtering and niche partitioning. However, the role of other factors, such as species-specific parasites, is still poorly understood. Along the riparian understory of a tropical forest, we explored niche occupation and coexistence between Chrysso intervales and Helvibis longicauda, two related syntopic web-building spiders...

Social wasps encompass species displaying diverse social organization regarding colony cycle, nest foundation, caste differences (from none to significant dimorphism) and number of reproductive queens. Current phylogenetic data suggests that sociality occured independently in the subfamily Stenogastrinae and in the Polistinae+Vespinae clade. In most species, including those with the simplest social organization, colony reproduction is monopolised by a single or few females. Since their nest mates can also develop ovaries and lay eggs, dominant females must somehow inhibit them from reproducing...

The sheep ked Melophagus ovinus is mainly found in Europe, Northwestern Africa, and Asia. Although M. ovinus is an important ectoparasite of sheep in many countries, the population genetics, molecular biology, and systematics of this ectoparasite remain poorly understood. Herein, we determined the mitochondrial (mt) genome of M. ovinus from Gansu Province, China (MOG) and compared with that of M. ovinus Xinjiang Uygur Autonomous Region, China (MOX). The mt genome sequence (15,044 bp) of M. ovinus MOG was significantly shorter (529 bp) than M...

Perinatal specimens of hadrosaurids discovered in the late 1970's by field crews from Princeton University were significant in providing evidence of the early ontogenetic stages in North American dinosaurs. These specimens from the Campanian (Upper Cretaceous) Two Medicine Formation of Montana consist of over a dozen skeletons referable to the saurolophine hadrosaurid Maiasaura peeblesorum , but never fully figured or described. Here, we provide a more complete documentation of the morphology of these specimens, along with an examination of variation during a large span of the development of saurolophine hadrosaurids...

Chikungunya Virus (CHIKV) is a single stranded positive sense enveloped RNA virus. Re-emergence of CHIKV caused a massive outbreak with severe clinical manifestation affecting multiple organs. The genetic diversity of CHIKV, which caused recurring outbreaks in India, was studied. Blood samples were collected from suspected human cases of CHIKV infection in Chennai, Tamil Nadu and three Northern districts of Kerala in Southern India during the CHIKV outbreak in 2009. A partial E2 gene segment was amplified by RT-PCR...

Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) mediates parasite sequestration to the cerebral microvasculature via binding of DBLβ domains to Intercellular Adhesion Molecule 1 (ICAM1) and is associated with severe cerebral malaria. In a cohort of 187 young children from Papua New Guinea (PNG), we examined baseline antibody levels to the ICAM1-binding PfEMP1 domain, DBLβ3PF11_0521 , in comparison to four control antigens including NTS-DBLα and CIDR1 domains from another group A variant and a group B/C variant...

Protected areas (PAs) that span elevational gradients enhance protection for taxonomic and phylogenetic diversity and facilitate species range shifts under climate change. We quantified the global protection of elevational gradients by analyzing the elevational distributions of 44,155 PAs in 1,010 mountain ranges using the highest resolution digital elevation models available. We show that, on average, mountain ranges in Africa and Asia have the lowest elevational protection, ranges in Europe and South America have intermediate elevational protection, and ranges in North America and Oceania have the highest elevational protection...

The morning glory family, Convolvulaceae, is globally important in medicine and food crops. The family has worldwide distribution in a variety of habitats; however, its fossil record is very poorly documented. The current fossil record suggests an origin in North America, which is in contrast to molecular data that indicate an East Gondwana origin. We report Ipomoea leaves from the late Paleocene (Thanetian; 58.7-55.8 million years ago) of India, which was a part of East Gondwana during this time. This is the earliest fossil record for both the family Convolvulaceae and the order Solanales...

All more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1-5' (DNA barcode fragment), cox1-3', and rrnL...

Superoxide dismutases (SODs) are among the most important antioxidant enzymes and show great potential in preventing adverse effects during therapeutic trials. In the present study, cloning, expression, and characterization of a novel Cu,Zn superoxide dismutase (Ps-Cu,Zn-SOD) from a hadal sea cucumber ( Paelopatides sp.) were reported. Phylogenetic analysis showed that Ps-Cu,Zn-SOD belonged to a class of intracellular SOD. Its K m and V max were 0.0258 ± 0.0048 mM and 925.1816 ± 28.0430 units/mg, respectively...

Catalases reduce oxidative stress by degrading hydrogen peroxide to molecular oxygen and water. The presence of heme-dependent or manganese-dependent catalases was observed for a long time in lactic acid bacteria (LAB) but, to date, knowledge on the factors affecting gene expression and enzymatic functionality are limited to a very few strains. In this study, the effect of atmosphere of incubation (not aerated static growth vs aerated shaken growth) and supplementation with Fe2+ , hemin, Mn2+ or their combinations on the catalase production of respiration-competent strain Lactobacillus casei N87 was evaluated using a 24 factorial design...

OBJECTIVES: Multiple invasive group A streptococcal (GAS) infections were reported to public health by a skilled nursing facility (Facility A) in Illinois between May 2014 and August 2016. Cases continued despite interventions including antibiotic prophylaxis for all residents and staff. Two other geographically close facilities reported contemporaneous outbreaks of GAS. We investigated potential reasons for ongoing transmission. METHODS: We obtained epidemiologic data from chart review of cases and review of facility and public health records from previous investigations into the outbreak...